Even when they are taught to think only in science lessons, their performance improves in English and maths, the report from King's College London says.
The five-year study involving 4,500 pupils compared the performance of those taught "thinking science" with those who were not.
Researchers found that the result was the equivalent of raising the national average of those getting grade C and above at GCSE in science from 42.8 per cent to 63.8 per cent. In maths, the figure would rise from 40.2 to 56.4 per cent and in English from 50.4 to 63 per cent.
In the national tests for 14-year-olds, schools in the programme more than doubled the proportion of pupils getting the higher grades in all three subjects.
Lessons in the Cognitive Acceleration through Science programme encourage children to think about their own thinking and to discuss with each other how they tackled and solved problems set by the teacher.
The programme, based on the principles of learning established by the educational psychologists Piaget and Vygotsky, is offered to pupils in the first two years of secondary school. Time spent learning to think has to be deducted from time normally spent acquiring scientific knowledge.
Dr Philip Adey, director for the Advancement of Thinking at King's, said: "The aim is to get children to think about their own thinking, to ask what they thought about something when they started the lesson, what they think now and why it has changed."
The lessons explore variables, proportionality, ratio, probability and correlation.
In probability, for instance, the teacher may start a discussion about risk with five cups of tea and ask whether it makes any difference whether the milk is put in first. Pupils have to guess whether the milk was put in first in each cup of tea. The teacher asks how many the pupil has to get right before the rest of the class believe he or she can guess correctly.
Dr Adey said: "The issue is not how many does she have to get right before you believe her. It is one of confidence and the level of risk you are prepared to accept. You can move on then to discuss the risk of lung cancer or leukaemia."
Professor Michael Shayer, programme director, suggested that the method might affect pupils' performance in English as well as science because it taught them how to handle many variables. "In an English comprehension you are asking how does this relate to that."
Marina Lecky, who has taught the programme at Grey Coat Hospital School in London, said teachers had to learn to ask children a question to help them to move on rather than giving them the answer. Her class had told her that their brains hurt after a "thinking" science lesson.Reuse content